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Escherichia coli YtfE E125L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298.15 Tris-HCl, PEG 4000, Magnesium chloride, Sodium Chloride
Crystal Properties Matthews coefficient Solvent content 2.59 59.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.79 α = 90 b = 49.608 β = 100.143 c = 87.819 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2017-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.87 53.2 99.8 0.082 0.096 0.049 0.999 9.7 3.7 41865 30.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.98 99.74 1.232 0.767 0.36
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5FNN 1.87 53.2 1.35 41842 2037 99.77 0.1838 0.1824 0.189 0.2106 0.2118 48.76
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.9962 f_angle_d 0.5287 f_chiral_restr 0.035 f_plane_restr 0.0033 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3460 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Coot model building PHASER phasing